1. Changed the kobolds to elven brigands. They're using the catacomb as a base of operations, and the lingering transmutation magic is affecting all of them, physically and mentally. Their skin and hair have turned jet black (a bit of misdirection, as the players may think drow, though the hair should tip them off that things aren't standard). The elves have developed a bit of paranoia and xenophobia, simultaneously hating outsiders and mistrusting each other.
2. The main BBEG ("Her Ladyship") will be the female elf leading the group. The magic has imbued her with significant power, including a template very similar to the ebon servitor template from the original Book of Templates. I picture her face as ever-shifting, with no permanent appearance.
3. Idruma will become a blind oracle (again, from BoT), held captive by Her Ladyship. Idruma will forsee that the party are coming, but will she warn her captor? Depends if she thinks she'll get a better deal from the party.
4. A creature of my own design based on the phantom fungus from the MM. Basically, it's an intelligent plant that is permanently invisible. The sap from its skin turns organic matter invisible for a short period, which means when it hits someone, they go invisible for a few rounds. The creature has blindsense, but I expect the players to be a bit freaked out at first, when their tanks start disappearing. It will likely use hit and run tactics, hoping to keep the party off balance. In fact, depending on the descriptions I use for the damage, they may never figure out what is happening to them until they literally trip over the thing.
5. The walls and floors of the catacombs are continually changing. Haven't really figured out what to do with this - I want something that will creep out the players and keep them on their toes, without really hurting them. Maybe something similar to Star Trek's holodeck, with rooms appearing to be forests and such...
6. Still haven't decided if I'll keep the wild magic areas, or just give the brigands random effects that hit in times of stress, such as combat. If I do keep them, I'll reduce them to one or two areas, so the players don't become blase about them.